V4: Tools for task views
Introduction
RWsearch stands for « Search in R packages, task views, CRAN and in the Web ».
This vignette introduces the following features cited in the README file:
.12. Provide some tools for task view maintenance: Detect the packages recently added to or updated in CRAN, check if they match some keywords, check if they are already recorded in a given task view.
.5. Display the results as a list or as a table in the console or in the browser and save them as txt, md, html, tex or pdf files.
Task views
Task views are an important part of CRAN as they help R users to find the packages that match their needs. Task view pages are maintained by volunteers who update the pages and upload them to CRAN with the package ctv.
RWsearch focuses on detecting the (old and new) packages that could be added to the task views.
View, download, load and explore task views
As a preliminary, all task views can be read on-line with the instruction:
RWsearch provides the functions
tvdb_down() and
tvdb_load() to download a file renamed or
load the task views in .GlobalEnv as a list named
tvdb. Four functions are available to explore
this list: tv_vec(),
tvdb_dfr(),
tvdb_list(),
tvdb_pkgs().
crandb_down(), tvdb_down(), crandb_load(), tvdb_load()
In an empty directory, the two files crandb.rda and tvdb.rda, which are cleaned versions of the files /web/packages/packages.rds and /src/contrib/Views.rds, must be downloaded from CRAN. Once downloaded, the files are automatically loaded with names crandb (a data.frame) and tvdb (a list) in .GlobalEnv. The most recently updated task view can have an older date than the saved date.
crandb_down()
# $newfile
# [1] "crandb.rda saved and loaded. 17672 packages listed between 2006-03-15 and 2021-06-02"
tvdb_down()
# [1] "tvdb.rda saved. tvdb loaded. 41 task views listed between 2015-01-07 and 2021-06-02"
ls()
# [1] "crandb" "tvdb" If the files already exist in one specific directory, they can be loaded. Here are the numbers for February 2019, June 2021 and September 2024:
crandb_load(filename = "crandb-2024-0926.rda")
# "crandb loaded. 13752 packages listed between 2006-03-15 and 2019-02-25"
# "crandb loaded. 17672 packages listed between 2006-03-15 and 2021-06-02"
# "crandb loaded. 21403 packages listed between 2008-09-08 and 2024-09-26"
tvdb_load(filename = "tvdb-2024-0926.rda")
# tvdb loaded. 39 task views listed between 2015-01-07 and 2019-02-25
# tvdb loaded. 41 task views listed between 2015-01-07 and 2021-06-02
# tvdb loaded. 45 task views listed between 2021-12-29 and 2024-09-25tvdb_vec(), tvdb_dfr()
Functions tv_vec() and
tvdb_dfr() list the task views available
and their topics.
There were 39 task views in February 2019, 41 task views in June 2021 and 45 task views in September 2024. The latest two task views are TeachingStatistics and Tracking. The largest task view is Time Series with 273 packages in February 2019, 326 in June 2021 and 402 packages in September 2024. Many task views are maintained a minima and list less packages than in February 2019 due to packages archived by CRAN. Task views need to be reconsidered.
tvdb_vec()
# [1] "ActuarialScience" "Agriculture" "Bayesian"
# [4] "CausalInference" "ChemPhys" "ClinicalTrials"
# [7] "Cluster" "Databases" "DifferentialEquations"
# [10] "Distributions" "DynamicVisualizations" "Econometrics"
# [13] "Environmetrics" "Epidemiology" "ExperimentalDesign"
# [16] "ExtremeValue" "Finance" "FunctionalData"
# [19] "GraphicalModels" "HighPerformanceComputing" "Hydrology"
# [22] "MachineLearning" "MedicalImaging" "MetaAnalysis"
# [25] "MissingData" "MixedModels" "ModelDeployment"
# [28] "NaturalLanguageProcessing" "NumericalMathematics" "OfficialStatistics"
# [31] "Omics" "Optimization" "Pharmacokinetics"
# [34] "Phylogenetics" "Psychometrics" "ReproducibleResearch"
# [37] "Robust" "Spatial" "SpatioTemporal"
# [40] "SportsAnalytics" "Survival" "TeachingStatistics"
# [43] "TimeSeries" "Tracking" "WebTechnologies" tv2 <- tvdb_dfr()
tv2 <- tv2[order(tv2$npkgs),]
rownames(tv2) <- NULL
print(tv2, right=FALSE)
# version npkgs name topic (xx packages in June 2021)
# 1 2022-08-24 31 ModelDeployment Model Deployment with R (32)
# 2 2022-08-31 33 MedicalImaging Medical Image Analysis (23)
# 3 2023-05-25 34 DifferentialEquations Differential Equations (28)
# 4 2023-04-05 39 GraphicalModels Graphical Models (40)
# 5 2024-06-06 41 ActuarialScience Actuarial Science (new)
# 6 2023-11-04 41 ExtremeValue Extreme Value Analysis (24)
# 7 2024-08-22 43 Pharmacokinetics Analysis of Pharmacokinetic Data (18)
# 8 2023-02-23 45 Databases Databases with R (37)
# 9 2024-09-25 47 DynamicVisualizations Dynamic Visualizations and Interactive Graphics (34)
# 10 2023-03-07 49 Tracking Processing and Analysis of Tracking Data (49)
# 11 2023-07-01 52 Robust Robust Statistical Methods (58)
# 12 2024-08-01 53 TeachingStatistics Teaching Statistics (45)
# 13 2021-12-29 55 ClinicalTrials Clinical Trial Design, Monitoring, and Analysis (61)
# 14 2024-06-17 57 FunctionalData Functional Data Analysis (40)
# 15 2023-09-12 60 NaturalLanguageProcessing Natural Language Processing (55)
# 16 2022-10-01 72 SpatioTemporal Handling and Analyzing Spatio-Temporal Data (92)
# 17 2024-09-19 79 SportsAnalytics Sports Analytics (new)
# 18 2024-05-13 91 HighPerformanceComputing High-Performance and Parallel Computing with R (92)
# 19 2024-09-12 93 Epidemiology Epidemiology (new)
# 20 2024-01-29 98 ChemPhys Chemometrics and Computational Physics (81)
# 21 2023-12-18 100 Environmetrics Analysis of Ecological and Environmental Data (94)
# 22 2023-04-05 102 ExperimentalDesign Design of Experiments (DoE) & Analysis of Experimental Data (112)
# 23 2024-01-30 105 Phylogenetics Phylogenetics (82)
# 24 2024-08-20 107 Cluster Cluster Analysis & Finite Mixture Models (106)
# 25 2023-07-20 113 MachineLearning Machine Learning & Statistical Learning (96)
# 26 2024-09-25 114 ReproducibleResearch Reproducible Research (92)
# 27 2024-07-27 126 NumericalMathematics Numerical Mathematics (115)
# 28 2024-03-08 127 Hydrology Hydrological Data and Modeling (98)
# 29 2024-07-05 137 Optimization Optimization and Mathematical Programming (136)
# 30 2024-04-09 140 OfficialStatistics Official Statistics & Survey Statistics (132)
# 31 2023-08-04 152 CausalInference Causal Inference (new)
# 32 2024-06-03 152 Econometrics Econometrics (144)
# 33 2024-09-19 154 Finance Empirical Finance (156)
# 34 2024-09-12 168 Agriculture Agricultural Science (new)
# 35 2024-05-08 168 MixedModels Mixed, Multilevel, and Hierarchical Models in R (111)
# 36 2024-09-10 184 MetaAnalysis Meta-Analysis (154)
# 37 2023-02-18 188 WebTechnologies Web Technologies and Services (204)
# 38 2024-06-18 198 Spatial Analysis of Spatial Data (184)
# 39 2023-07-17 200 Bayesian Bayesian Inference (138)
# 40 2023-09-10 223 Survival Survival Analysis (251)
# 41 2023-12-15 230 Psychometrics Psychometric Models and Methods (242)
# 42 2024-09-25 254 Omics Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics (new)
# 43 2024-06-20 269 MissingData Missing Data (164)
# 44 2024-09-25 318 Distributions Probability Distributions (252)
# 45 2024-09-09 402 TimeSeries Time Series Analysis (326) tvdb_list(), tvdb_pkgs()
tv_list() lists all task views and
their packages. tvdb_dfr() lists the
packages of the task views selected by the user.
tvdb_list()
$ActuarialScience
# [1] "actuar" "actuaRE" "ActuarialM"
# ...
# [40] "tweedie" "WH"
# ...
# ...
# $WebTechnologies
# [1] "ajv" "analogsea" "arrow" "aRxiv"
# ...
# [185] "xslt" "yaml" "yhatr" "zen4R" tvdb_pkgs(ChemPhys, Distributions, Robust)
# $ChemPhys
# [1] "AeroSampleR" "albatross" "ALS" "AquaEnv" "astrodatR"
# ...
# [96] "units" "varSelRF" "webchem"
#
# $Distributions
# [1] "actuar" "AdMit" "AEP" "agricolae" "ald" "alphastable"
# ...
# [317] "zipfextR" "zipfR"
#
# $Robust
# [1] "clubSandwich" "cluster" "clusterSEs" "complmrob" "covRobust"
# ...
# [51] "walrus" "WRS2"Counting the number of referred packages
The largest task view has referred 326 packages (273 in February 2019). All task views have referred 4298 (4021) packages but only 3451 (3221) unique packages. This is 19.5 % (down from 23.4 % in 2019) of the total number of packages currently in CRAN. The task is immense if we want to refer all packages.
nrow(crandb)
# 21403 (17672 in June 2021, 13752 in February 2019)
max(sapply(tvdb_list(), length))
# [1] 402 (326 in June 2021, 273 in February 2019)
length(unlist(tvdb_list()))
# [1] 5544 (4298 in June 2021, 4021 in February 2019)
length(unique(unlist(tvdb_list())))
# [1] 4646 (3451 in June 2021, 3221 in February 2019)Task view maintenance
RWsearch focuses on detecting the (old and new) packages that could be added to the task views.
Function s_crandb_tvdb() combines many
functions of RWsearch. It searchs packages in
crandb by keywords and checks if the found packages are
referred in the selected task view and installed in the computer (in the
/site-library directory).
The example presented below refers to the Distributions task view.
s_crandb_tvdb()
The output of s_crandb_tvdb() is a list
with the following items:
- spkgs: packages that match the keywords.
- inTV: packages that are already referred in the selected task view.
- notinTV: packages that are not (yet) referred in the task view.
- inTV_in: packages that are referred and installed in the computer.
- inTV_un: packages that are referred but not installed in the computer.
- notinTV_in: packages that are not referred and installed in the computer.
- notinTV_un: packages that are neither referred nor installed in the computer.
keywords <- cnsc(probability, distribution)
(lst <- s_crandb_tvdb(char = keywords, tv = "Distributions",
from = -15, to = "2024-09-26", select = "PT"))
# $spkgs
# [1] "bayesSurv" "changepointTests" "CholWishart" "degreenet"
# [5] "DiscreteDists" "distfromq" "distributional" "distributions3"
# [9] "e1071" "eSDM" "evd" "mniw"
# [13] "modelbpp" "mvgb" "MVT" "PhaseType"
# [17] "PoissonBinomial" "ream" "scoringRules" "TLIC"
# $inTV
# [1] "degreenet" "distributional" "distributions3" "e1071" "evd"
# [6] "mniw" "mvgb" "MVT" "PoissonBinomial"
# $notinTV
# [1] "bayesSurv" "changepointTests" "CholWishart" "DiscreteDists"
# [5] "distfromq" "eSDM" "modelbpp" "PhaseType"
# [9] "ream" "scoringRules" "TLIC"
# $inTV_in
# [1] "distributional" "e1071" "evd"
# $inTV_un
# [1] "degreenet" "distributions3" "mniw" "mvgb" "MVT"
# [6] "PoissonBinomial"
# $notinTV_in
# character(0)
# $notinTV_un
# [1] "bayesSurv" "changepointTests" "CholWishart" "DiscreteDists"
# [5] "distfromq" "eSDM" "modelbpp" "PhaseType"
# [9] "ream" "scoringRules" "TLIC" Visualize the unreferred packages
A first assesment of the packages that match the keywords can be done
with p_table2(). Consider also
p_display5() to read the results in the
browser.
p_table2(), p_display5()
p_table2(lst$notinTV)
# Package Title
# 1153 bayesSurv Bayesian Survival Regression with Flexible Error and Random Effects Distributions
# 2378 changepointTests Change Point Tests for Joint Distributions and Copulas
# 2455 CholWishart Cholesky Decomposition of the Wishart Distribution
# 4324 DiscreteDists Discrete Statistical Distributions
# 4366 distfromq Reconstruct a Distribution from a Collection of Quantiles
# 5386 eSDM Ensemble Tool for Predictions from Species Distribution Models
# 11363 modelbpp Model BIC Posterior Probability
# 13551 PhaseType Inference for Phase-Type Distributions
# 15449 ream Density, Distribution, and Sampling Functions for Evidence Accumulation Models
# 17177 scoringRules Scoring Rules for Parametric and Simulated Distribution Forecasts
# 19865 TLIC The LIC for T Distribution Regression Analysis
From the package titla above and the DESCRIPTION in the html page, packages CholWishart, DiscreteDists, distfromq and ream deserve further exploration.
p_page(), p_pdfweb()
4 packages is a reasonnable number. We can open the CRAN/index.html pages and CRAN/manual.pdf files in the browser. Alternatively, consider downloading the documentation of these packages.
pkgs <- cnsc(CholWishart, DiscreteDists, distfromq, ream)
p_page(pkgs)
## read the 4 html pages launched in your browser
p_pdfweb(pkgs)
## read the 4 pdf pages launched in your browser
p_down(pkgs)
## read the files saved in the current directory
The pdf files and the vignettes give all expected information and help decide whether or not include the package in the task view